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Genomic Analyses Offer Clues to Bioethanol-Producing Yeast

NEW YORK (GenomeWeb News) – In a pair of recent Genome Research papers, two research teams applied genetic and genomic approaches to learn more about an industrial Saccharomyces cerevisiae strain called PE-2 and other yeast strains that are being used to produce biofuels.

The PE-2 strain, which ferments sugar cane, is used by nearly a third of Brazilian distilleries. The microbe has garnered attention in biofuel circles, since Brazilian bioethanol projects typically rely on sugar cane as a feedstock rather than grains.

In the first of these studies, published online early last month, researchers from the US and Brazil used Roche 454 and Illumina platforms to do massively parallel, whole-genome shotgun sequencing of a haploid PE-2 strain. The group also used array comparative genomic hybridization and other methods to genetically characterize a diploid PE-2 strain.

By comparing the PE-2 genome with three previously sequenced S. cerevisiae strains, that team found several structural rearrangements and insertions in the bioethanol-producing PE-2 strain, as well as at least 38 genes that aren't found in a laboratory S. cerevisiae strain.

In particular, the researchers noted, rearrangements in the PE-2 genome almost always occurred at the ends of chromosomes, suggesting these regions are important for the strain's adaptation to an industrial setting. And based on PE-2 genome sequence and architecture, they suggested such rearrangements might amplify stress-related genes.

"Our data suggest a general chromosome organization in which the central core sectors, harboring essential genes, are refractory to rearrangements, while the peripheral regions are highly plastic and are free to undergo ectopic recombination," senior author Goncalo Pereira, a researcher at the Universidade Estadual de Campinas at Sao Paulo, and his co-authors wrote.

Meanwhile, in a paper appearing online in Genome Research today, another American and Brazilian research team used array CGH to find copy number variations in the genome of PE-2 and four other bioethanol-producing S. cerevisiae strains: BG-1, CAT-1, SA-1, and VR-1.

When they looked at the genetic variation in these five yeast strains, the team found 72 genes that were affected by CNVs in bioethanol strains but not in reference yeast strains or other industrial strains.

And while many of the CNVs they detected in industrial yeast strains led to reduced gene copy number, the researchers found that biofuel specific CNVs often amplified parts of the genome. For instance, they detected CNVs that created extra copies of SNO and SNZ genes — genes found at the ends of chromosomes that contribute to vitamin B6 and vitamin B1 synthesis.

The team's subsequent experiments suggest that having extra copies of these genes improves yeast growth under industrial conditions, consistent with the role of these vitamins in yeast growth, sugar use, and bioethanol production.

"We show that increased copy number of these genes confers the ability to grow more efficiently under the repressing effects of thiamin [vitamin B1], especially in medium lacking pyridoxine [vitamin B6] and with high sugar concentrations," senior author Gavin Sherlock, a genetics researcher at Stanford University, and his co-authors wrote.

Sherlock and his team suggest these results also point to a potential bioavailability problem for vitamin B6 and B1 in industrial bioethanol production systems.

Overall, both research teams highlighted the value of such genomic studies for helping to unravel the genetic components of bioethanol-production by natural yeast strains — findings that may aid efforts to engineer new bioethanol-producing microbes.

"Decades of experience in the development of industrial strains have convincingly demonstrated that any large-scale attempt to introduce genetically modified yeast strains in the bioethanol industry will be futile unless they are based on naturally adapted strains," Pereira and his co-authors wrote.

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